Example data for IM-TORNADO

This is the documentation for the example data provided to test the IM-TORNADO 16S pipeline.

Introduction

The example data files in this directory represent a minimal data set for testing of the pipeline (and a tutorial of sorts). It consists of five human stool samples (part of a larger study), sequenced in an Illumina MiSeq instrument using 500 bp (2 x 250 bp) chemistry. The 16S region amplified was V3 to V5 (357F to 926R). These are the raw deumtiplexed files as received from our sequencing facility. These kind of files is what IM-TORNADO expects as input.

Contents

• 10 fastq files (5 for R1 and R2, respectively)
• metadata/mapping file, "example.mapping.txt"
• results-example directory, with the output of a run of the pipeline, for comparison purposes
• workspace-example directory, with the remaining intermediate files not deleted by the pipeline upon completion, for comparison purposes
• This README.md file

Instructions

Follow the basic instructions for running the pipeline, as explained in the documentation. In short,

• Copy the "tornado-params.sh" configuration file from the scripts directory
• Edit the file accordingly
• Run the pipeline with "tornado_run_pipeline.sh" making sure the bin directory of the pipeline is in the PATH

Notes

In our tests, this dataset finished in about 7 minutes and used 1.6 GB of RAM. Your results may vary.

You can use the output files in other programs, such as QIIME, phyloseq or the metagenassist.ca website, mostly without modifications. The files left in the workspace directory can be used as input for picrust (processed with QIIME first. See their tutorial).